From: Luis Cunha (
Date: Sat Nov 01 2008 - 19:43:30 CDT

I'm doing a simulation on NAMD using the ff99SB AMBER force field. According to NAMD instructions to use the AMBER ff with NAMD ( the following NAMD parameters:

rigidTolerance 0.0001
1-4scaling 1.0

    should be changed to AMBER compatible values:

rigidTolerance 0.0005
1-4scaling 0.83333

However, while simulations with the first set maintain the protein conformation, simulations with the second set (recommended when using amber ff) destroy a few helices(not all!; the helix residues break apart into a random coil).

Has anyone experienced this problem? What am I doing wrong?

Thank you in advance for your help,

Luis Cunha, PhD
Dept. of Human Genetics
Mount Sinai School of Medicine of the New York University

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:02 CST